URL: <http://gna.org/bugs/?7241> Summary: Problem with reading RNA PDBs Project: relax Submitted by: viochemist Submitted on: Friday 09/29/2006 at 17:23 Category: None Priority: 5 - Normal Severity: 4 - Important Status: None Privacy: Private Assigned to: None Originator Name: Originator Email: Open/Closed: Open Release: 1.2.7 Operating System: GNU/Linux _______________________________________________________ Details: Full post at https://mail.gna.org/public/relax-users/2006-09/msg00041.html <481156b20609281057o4fe80f47wc1dda6ea6516498d@xxxxxxxxxxxxxx> See below for pdb and input. Lines changed in full_analysis.py: 128: 'sphere' 174: pdb(name, 'etar.pdb', heteronuc='N1', proton='H1') 380: pdb(name, 'etar.pdb', heteronuc='N1', proton='H1') $ python relax full_analysis.py Results: relax> run.create(run='sphere', run_type='mf') relax> results.read(run='sphere', file='results', dir='local_tm/aic', format='columnar') Opening the file 'local_tm/aic/results.bz2' for reading. relax> model_free.remove_tm(run='sphere', res_num=None) relax> pdb(run='sphere', file='etar.pdb', dir=None, model=None, heteronuc='N1', proton='H1', load_seq=1) Loading all structures from the PDB file. Structure('etar.pdb', model=1): Nucleotide chain of length 1 Calculating unit XH vectors. Structure 1 Traceback (most recent call last): File "relax", line 458, in ? Relax() File "relax", line 170, in __init__ self.interpreter.run() File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 213, in run run_script(intro=self.relax.intro_string, local=self.local, script_file=self.relax.script_file, quit=1) File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 388, in run_script console.interact(intro, local, script_file, quit) File "/local/home/viochem/relax_1.2.7/prompt/interpreter.py", line 340, in interact_script execfile(script_file, local) File "full_analysis.py", line 412, in ? Main() File "full_analysis.py", line 174, in __init__ pdb(name, 'etar.pdb', heteronuc='N1', proton='H1') File "/local/home/viochem/relax_1.2.7/prompt/pdb.py", line 129, in pdb self.relax.generic.pdb.load(run=run, file=file, dir=dir, model=model, heteronuc=heteronuc, proton=proton, load_seq=load_seq) File "/local/home/viochem/relax_1.2.7/generic_fns/pdb.py", line 198, in load self.vectors() File "/local/home/viochem/relax_1.2.7/generic_fns/pdb.py", line 229, in vectors pdb_residues = self.relax.data.pdb[self.run].structures[i].peptide_chains[0].residues IndexError: list index out of range ================== Simplify the PDB ================== Identical output. Curious line is at the end where it says: self.relax.data.pdb[self.run].structures[i].peptide_chains[0].residues ************ My Input ************ R1: Num Name Value Error 1 G 0.738 0.022 R2: Num Name Value Error 1 G 23.74 0.33 NOE: Num Name Value Error 1 G 0.686 0.018 ******************* whole residue PDB ******************* etar.pdb MODEL 1 ATOM 1 P G 1 -2.918 -16.615 -49.930 1.00 0.00 P ATOM 2 O1P G 1 -3.505 -17.162 -51.178 1.00 0.00 O ATOM 3 O2P G 1 -1.490 -16.217 -50.016 1.00 0.00 O ATOM 4 O5' G 1 -3.782 -15.376 -49.413 1.00 0.00 O ATOM 5 O3' G 1 -6.236 -12.842 -50.659 1.00 0.00 O ATOM 6 C1' G 1 -5.187 -12.610 -47.168 1.00 0.00 C ATOM 7 C2' G 1 -5.658 -11.918 -48.451 1.00 0.00 C ATOM 8 C3' G 1 -5.445 -13.010 -49.490 1.00 0.00 C ATOM 9 C4' G 1 -5.829 -14.263 -48.722 1.00 0.00 C ATOM 10 C5' G 1 -5.195 -15.566 -49.213 1.00 0.00 C ATOM 11 O4' G 1 -5.357 -14.014 -47.368 1.00 0.00 O ATOM 12 O2' G 1 -7.043 -11.646 -48.287 1.00 0.00 O ATOM 13 N2 G 1 -3.764 -7.849 -44.958 1.00 0.00 N ATOM 14 O6 G 1 0.310 -9.848 -46.253 1.00 0.00 O ATOM 15 C6 G 1 -0.956 -9.976 -46.221 1.00 0.00 C ATOM 16 C5 G 1 -1.781 -11.085 -46.692 1.00 0.00 C ATOM 17 N7 G 1 -1.395 -12.320 -47.327 1.00 0.00 N ATOM 18 C8 G 1 -2.570 -12.950 -47.544 1.00 0.00 C ATOM 19 N9 G 1 -3.710 -12.226 -47.102 1.00 0.00 N ATOM 20 C4 G 1 -3.184 -11.015 -46.550 1.00 0.00 C ATOM 21 N3 G 1 -3.964 -9.991 -45.989 1.00 0.00 N ATOM 22 C2 G 1 -3.196 -8.955 -45.542 1.00 0.00 C ATOM 23 N1 G 1 -1.768 -8.924 -45.646 1.00 0.00 N ATOM 24 H1' G 1 -5.799 -12.337 -46.307 1.00 0.00 H ATOM 25 H2' G 1 -5.074 -11.028 -48.681 1.00 0.00 H ATOM 26 H3' G 1 -4.411 -13.056 -49.833 1.00 0.00 H ATOM 27 H4' G 1 -6.911 -14.367 -48.796 1.00 0.00 H ATOM 28 1H5' G 1 -5.363 -16.346 -48.472 1.00 0.00 H ATOM 29 2H5' G 1 -5.663 -15.858 -50.154 1.00 0.00 H ATOM 30 HO2' G 1 -7.555 -12.532 -48.168 1.00 0.00 H ATOM 31 1H2 G 1 -4.818 -7.792 -44.843 1.00 0.00 H ATOM 32 2H2 G 1 -3.151 -7.049 -44.622 1.00 0.00 H ATOM 33 H8 G 1 -2.640 -13.960 -48.032 1.00 0.00 H ATOM 34 H1 G 1 -1.267 -8.064 -45.271 1.00 0.00 H ENDMDL END **************** Simplified PDB **************** MODEL 1 ATOM 23 N1 G 1 -1.768 -8.924 -45.646 1.00 0.00 N ATOM 34 H1 G 1 -1.267 -8.064 -45.271 1.00 0.00 H ENDMDL END _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?7241> _______________________________________________ Message sent via/by Gna! http://gna.org/